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- PDB-9bug: Hydrolase domain of Chitinase 1 from Enterobacter cloacae -

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Basic information

Entry
Database: PDB / ID: 9bug
TitleHydrolase domain of Chitinase 1 from Enterobacter cloacae
ComponentsExochitinase 1
KeywordsHYDROLASE / chitinase / chitobiosidase / GH18 / hydrolase domain
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEnterobacter cloacae complex sp. ECNIH14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDalton, J.A.T. / Frkic, R.L. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Hydrolase domain of Chitinase 1 from Enterobacter cloacae
Authors: Dalton, J.A.T. / Frkic, R.L. / Jackson, C.J.
History
DepositionMay 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exochitinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1089
Polymers45,5261
Non-polymers5828
Water9,764542
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.057, 90.448, 54.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Exochitinase 1 / Glycoside hydrolase family 18 protein


Mass: 45526.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae complex sp. ECNIH14 (bacteria)
Gene: FHC55_13665 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA41LJJ9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 % (w/v) PEG 8000, 0.1 M Sodium Cacodylate, 0.2 M Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.3→46.73 Å / Num. obs: 99381 / % possible obs: 97.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.086 / Χ2: 0.99 / Net I/σ(I): 14.4 / Num. measured all: 1342291
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 96 % / Redundancy: 13.9 % / Rmerge(I) obs: 2.258 / Num. measured all: 66339 / Num. unique obs: 4768 / CC1/2: 0.652 / Rpim(I) all: 0.623 / Rrim(I) all: 2.343 / Χ2: 1 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→46.73 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 4994 5.03 %
Rwork0.157 --
obs0.1583 99316 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 38 542 3730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.944
X-RAY DIFFRACTIONf_dihedral_angle_d14.4591222
X-RAY DIFFRACTIONf_chiral_restr0.078485
X-RAY DIFFRACTIONf_plane_restr0.007603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.35061510.3243038X-RAY DIFFRACTION96
1.31-1.330.32971510.28943098X-RAY DIFFRACTION96
1.33-1.350.30391950.26532998X-RAY DIFFRACTION96
1.35-1.360.28661750.25973053X-RAY DIFFRACTION96
1.36-1.380.26591660.23743027X-RAY DIFFRACTION96
1.38-1.40.24081740.2193097X-RAY DIFFRACTION96
1.4-1.420.2321480.20683039X-RAY DIFFRACTION97
1.42-1.440.21781830.19553085X-RAY DIFFRACTION97
1.44-1.460.25191310.18833116X-RAY DIFFRACTION97
1.46-1.490.19791860.18023060X-RAY DIFFRACTION97
1.49-1.510.22711490.17683106X-RAY DIFFRACTION97
1.51-1.540.20081500.17883090X-RAY DIFFRACTION97
1.54-1.570.1981570.16893125X-RAY DIFFRACTION97
1.57-1.60.22671940.16673105X-RAY DIFFRACTION97
1.6-1.640.21141790.15443099X-RAY DIFFRACTION98
1.64-1.680.17461700.14833123X-RAY DIFFRACTION98
1.68-1.720.19531770.14483127X-RAY DIFFRACTION98
1.72-1.760.18831910.14473124X-RAY DIFFRACTION98
1.76-1.820.16331510.14443167X-RAY DIFFRACTION98
1.82-1.870.16511560.14923157X-RAY DIFFRACTION98
1.87-1.940.1911230.15933208X-RAY DIFFRACTION98
1.94-2.020.17341590.15333178X-RAY DIFFRACTION98
2.02-2.110.16121840.15073184X-RAY DIFFRACTION99
2.11-2.220.19271620.14423173X-RAY DIFFRACTION99
2.22-2.360.17621870.15233216X-RAY DIFFRACTION99
2.36-2.540.18071800.15343187X-RAY DIFFRACTION99
2.54-2.80.18881740.16183249X-RAY DIFFRACTION99
2.8-3.210.17261460.15483316X-RAY DIFFRACTION100
3.21-4.040.16571720.1393290X-RAY DIFFRACTION100
4.04-46.730.16231730.14573487X-RAY DIFFRACTION100

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